Data curation, coding style and sharing data

  • https://github.com/DrMattG/Oikos_Norway_2023
  • …/blob/main/messy_data.rds
  • …/blob/main/notReproducible.qmd

The Data life-cycle

Data handling & curation

Managing the “data life-cycle” within and beyond a project.

  • creating data
  • organising data
  • maintaining data

Data cleaning vs Data wrangling

Data cleaning is the process of removing incorrect, duplicate, or otherwise erroneous data from a dataset

Data wrangling changing the format to make it more useful for your analysis

Some R Functions that help data cleaning

{janitor}

library(tidyverse)
library(palmerpenguins)
library(janitor)

palmerpenguins::penguins_raw |>  names()
 [1] "studyName"           "Sample Number"       "Species"            
 [4] "Region"              "Island"              "Stage"              
 [7] "Individual ID"       "Clutch Completion"   "Date Egg"           
[10] "Culmen Length (mm)"  "Culmen Depth (mm)"   "Flipper Length (mm)"
[13] "Body Mass (g)"       "Sex"                 "Delta 15 N (o/oo)"  
[16] "Delta 13 C (o/oo)"   "Comments"           
janitor::clean_names(palmerpenguins::penguins_raw) |>  names()
 [1] "study_name"        "sample_number"     "species"          
 [4] "region"            "island"            "stage"            
 [7] "individual_id"     "clutch_completion" "date_egg"         
[10] "culmen_length_mm"  "culmen_depth_mm"   "flipper_length_mm"
[13] "body_mass_g"       "sex"               "delta_15_n_o_oo"  
[16] "delta_13_c_o_oo"   "comments"

{dplyr}

clean_penguins<-janitor::clean_names(palmerpenguins::penguins_raw)

dplyr::glimpse(clean_penguins)
Rows: 344
Columns: 17
$ study_name        <chr> "PAL0708", "PAL0708", "PAL0708", "PAL0708", "PAL0708~
$ sample_number     <dbl> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 1~
$ species           <chr> "Adelie Penguin (Pygoscelis adeliae)", "Adelie Pengu~
$ region            <chr> "Anvers", "Anvers", "Anvers", "Anvers", "Anvers", "A~
$ island            <chr> "Torgersen", "Torgersen", "Torgersen", "Torgersen", ~
$ stage             <chr> "Adult, 1 Egg Stage", "Adult, 1 Egg Stage", "Adult, ~
$ individual_id     <chr> "N1A1", "N1A2", "N2A1", "N2A2", "N3A1", "N3A2", "N4A~
$ clutch_completion <chr> "Yes", "Yes", "Yes", "Yes", "Yes", "Yes", "No", "No"~
$ date_egg          <date> 2007-11-11, 2007-11-11, 2007-11-16, 2007-11-16, 200~
$ culmen_length_mm  <dbl> 39.1, 39.5, 40.3, NA, 36.7, 39.3, 38.9, 39.2, 34.1, ~
$ culmen_depth_mm   <dbl> 18.7, 17.4, 18.0, NA, 19.3, 20.6, 17.8, 19.6, 18.1, ~
$ flipper_length_mm <dbl> 181, 186, 195, NA, 193, 190, 181, 195, 193, 190, 186~
$ body_mass_g       <dbl> 3750, 3800, 3250, NA, 3450, 3650, 3625, 4675, 3475, ~
$ sex               <chr> "MALE", "FEMALE", "FEMALE", NA, "FEMALE", "MALE", "F~
$ delta_15_n_o_oo   <dbl> NA, 8.94956, 8.36821, NA, 8.76651, 8.66496, 9.18718,~
$ delta_13_c_o_oo   <dbl> NA, -24.69454, -25.33302, NA, -25.32426, -25.29805, ~
$ comments          <chr> "Not enough blood for isotopes.", NA, NA, "Adult not~

{skimr}

out<-skimr::skim(palmerpenguins::penguins_raw)
out
Data summary
Name palmerpenguins::penguins_…
Number of rows 344
Number of columns 17
_______________________
Column type frequency:
character 9
Date 1
numeric 7
________________________
Group variables None

Variable type: character

skim_variable n_missing complete_rate min max empty n_unique whitespace
studyName 0 1.00 7 7 0 3 0
Species 0 1.00 33 41 0 3 0
Region 0 1.00 6 6 0 1 0
Island 0 1.00 5 9 0 3 0
Stage 0 1.00 18 18 0 1 0
Individual ID 0 1.00 4 6 0 190 0
Clutch Completion 0 1.00 2 3 0 2 0
Sex 11 0.97 4 6 0 2 0
Comments 290 0.16 18 68 0 10 0

Variable type: Date

skim_variable n_missing complete_rate min max median n_unique
Date Egg 0 1 2007-11-09 2009-12-01 2008-11-09 50

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
Sample Number 0 1.00 63.15 40.43 1.00 29.00 58.00 95.25 152.00 ▇▇▆▅▃
Culmen Length (mm) 2 0.99 43.92 5.46 32.10 39.23 44.45 48.50 59.60 ▃▇▇▆▁
Culmen Depth (mm) 2 0.99 17.15 1.97 13.10 15.60 17.30 18.70 21.50 ▅▅▇▇▂
Flipper Length (mm) 2 0.99 200.92 14.06 172.00 190.00 197.00 213.00 231.00 ▂▇▃▅▂
Body Mass (g) 2 0.99 4201.75 801.95 2700.00 3550.00 4050.00 4750.00 6300.00 ▃▇▆▃▂
Delta 15 N (o/oo) 14 0.96 8.73 0.55 7.63 8.30 8.65 9.17 10.03 ▃▇▆▅▂
Delta 13 C (o/oo) 13 0.96 -25.69 0.79 -27.02 -26.32 -25.83 -25.06 -23.79 ▆▇▅▅▂

{dplyr}

#Deduplication 
dim(clean_penguins)
[1] 344  17
clean_penguins_dup<-clean_penguins  |>  slice(rep(1:n(), each = 3)) 
dim(clean_penguins_dup)
[1] 1032   17
clean_penguins_undup<-distinct(clean_penguins_dup)
dim(clean_penguins_undup)
[1] 344  17

{naniar}

clean_penguins |> naniar::vis_miss()

Data validation

library(data.validator)

report <- data_validation_report()

between <- function(a, b) {
  function(x) { a <= x && x <= b }
}

validate(iris, name = "Verifying flower dataset") |>
  validate_if(Sepal.Length > 0, 
              description = "Sepal length is greater than 0") |>
  validate_cols(between(0, 4), 
                Sepal.Width, 
                description = "Sepal width is between 0 and 4") |>
  add_results(report)

#save_report(report)
#browseURL("validation_report.html")

print(report)
Validation summary: 
 Number of successful validations: 2
 Number of failed validations: 0
 Number of validations with warnings: 0

Advanced view: 


|table_name               |description                    |type    | total_violations|
|:------------------------|:------------------------------|:-------|----------------:|
|Verifying flower dataset |Sepal length is greater than 0 |success |               NA|
|Verifying flower dataset |Sepal width is between 0 and 4 |success |               NA|

Data wrangling

Transform to long format

library(tidyverse)
# this avoids tidyverse conflicts with the base function filter
conflicted::conflict_prefer("filter", "dplyr")
# Pivot longer 
penguins_long<-penguins |> 
  pivot_longer(contains("_"),
               names_to = c("part", "measure" , "unit"),
               names_sep = "_")

penguins_long
# A tibble: 1,376 x 8
   species island    sex     year part    measure unit   value
   <fct>   <fct>     <fct>  <int> <chr>   <chr>   <chr>  <dbl>
 1 Adelie  Torgersen male    2007 bill    length  mm      39.1
 2 Adelie  Torgersen male    2007 bill    depth   mm      18.7
 3 Adelie  Torgersen male    2007 flipper length  mm     181  
 4 Adelie  Torgersen male    2007 body    mass    g     3750  
 5 Adelie  Torgersen female  2007 bill    length  mm      39.5
 6 Adelie  Torgersen female  2007 bill    depth   mm      17.4
 7 Adelie  Torgersen female  2007 flipper length  mm     186  
 8 Adelie  Torgersen female  2007 body    mass    g     3800  
 9 Adelie  Torgersen female  2007 bill    length  mm      40.3
10 Adelie  Torgersen female  2007 bill    depth   mm      18  
# ... with 1,366 more rows

Transform to wide format

penguins_long |> 
  pivot_wider(names_from = species, 
              values_from = value)
# A tibble: 92 x 9
   island    sex     year part    measure unit  Adelie    Gentoo Chinstrap
   <fct>     <fct>  <int> <chr>   <chr>   <chr> <list>    <list> <list>   
 1 Torgersen male    2007 bill    length  mm    <dbl [7]> <NULL> <NULL>   
 2 Torgersen male    2007 bill    depth   mm    <dbl [7]> <NULL> <NULL>   
 3 Torgersen male    2007 flipper length  mm    <dbl [7]> <NULL> <NULL>   
 4 Torgersen male    2007 body    mass    g     <dbl [7]> <NULL> <NULL>   
 5 Torgersen female  2007 bill    length  mm    <dbl [8]> <NULL> <NULL>   
 6 Torgersen female  2007 bill    depth   mm    <dbl [8]> <NULL> <NULL>   
 7 Torgersen female  2007 flipper length  mm    <dbl [8]> <NULL> <NULL>   
 8 Torgersen female  2007 body    mass    g     <dbl [8]> <NULL> <NULL>   
 9 Torgersen <NA>    2007 bill    length  mm    <dbl [5]> <NULL> <NULL>   
10 Torgersen <NA>    2007 bill    depth   mm    <dbl [5]> <NULL> <NULL>   
# ... with 82 more rows

What’s going on?

No identifier for each observation so R puts all the values in a list. To solve this we need a unique row id.

penguins_long |> 
  mutate(sample=row_number()) |> 
  pivot_wider(names_from = species, 
              values_from = value)
# A tibble: 1,376 x 10
   island    sex     year part    measure unit  sample Adelie Gentoo Chinstrap
   <fct>     <fct>  <int> <chr>   <chr>   <chr>  <int>  <dbl>  <dbl>     <dbl>
 1 Torgersen male    2007 bill    length  mm         1   39.1     NA        NA
 2 Torgersen male    2007 bill    depth   mm         2   18.7     NA        NA
 3 Torgersen male    2007 flipper length  mm         3  181       NA        NA
 4 Torgersen male    2007 body    mass    g          4 3750       NA        NA
 5 Torgersen female  2007 bill    length  mm         5   39.5     NA        NA
 6 Torgersen female  2007 bill    depth   mm         6   17.4     NA        NA
 7 Torgersen female  2007 flipper length  mm         7  186       NA        NA
 8 Torgersen female  2007 body    mass    g          8 3800       NA        NA
 9 Torgersen female  2007 bill    length  mm         9   40.3     NA        NA
10 Torgersen female  2007 bill    depth   mm        10   18       NA        NA
# ... with 1,366 more rows

Tidy data

Tidy data principles

Messy data

Look at the messy data dataset. How would you go about cleaning this dataset?

messy_data <- readRDS(paste0(here::here(),"/NOS2023/Data_handling/messy_data.rds"))

messy_data |> data.table::data.table()
           Date    SEX      age    Species Name       lat      lon count
  1: 2023/02/01   male    Adult    Lagopus matu  9.123826 62.92628     5
  2:   02/02/23 Female Juvenile    Logopus muta  7.836517 61.70676     9
  3: 2023/02/01   male        J    Logopus muta  9.387262 63.84034    15
  4: 01-01-2023 female    ADULT Lagopus lagopus  9.609423 61.06334    14
  5: 01-01-2023   Male    ADULT    Lagopus matu  8.531654 63.44823    10
  6: 2023-02-01   Male        A    Lagopus muta 10.369053 62.60819    10
  7:   02/02/23 FEMALE JUVENILE    Lagopus muta  9.297162 62.71758    11
  8:   02-01-23 FEMALE    Adult Lagopus lagopus  6.479778 61.59151    15
  9: 2023-02-01 female Juvenile    Lagopus muta  7.879991 63.10879     4
 10:   02/02/23   MALE JUVENILE    Lagopus muta  6.794386 62.41039    14
 11: 2023/02/01 Female    ADULT    Lagopus matu 10.075820 62.14845     6
 12:   02-01-23   MALE        J Lagopas lagopus  9.368355 64.29196    13
 13: 2023/02/01 Female    ADULT    Lagopus matu 10.933222 63.08134     8
 14: 01-01-2023   Male        A    Logopus muta  9.508031 61.63579     7
 15:   02/02/23   MALE JUVENILE    Logopus muta 10.925062 62.59583     4
 16:   02/02/23 female        A Lagopus lagopus  9.279532 62.91511    11
 17:   02/02/23   male        J Lagopus lagopus  9.139805 65.96236    10
 18: 2023-02-01   male Juvenile Lagopas lagopus 10.119368 62.39573    15
 19:   02-01-23   MALE    Adult    Lagopus matu  7.847859 64.10893    10
 20: 2023-02-01   male JUVENILE    Lagopus muta 10.732284 64.42712    13
 21: 2023/02/01 Female        A Lagopas lagopus  8.541997 62.14247    14
 22:   02/02/23   male        J    Logopus muta  9.220419 62.62880    13
 23:   02-01-23 female JUVENILE Lagopus lagopus  9.624997 63.91689    13
 24: 01-01-2023 female    Adult Lagopas lagopus  8.769459 62.61416     9
 25: 01-01-2023 FEMALE    ADULT    Lagopus matu  9.011462 64.40237     2
 26:   02-01-23   MALE    ADULT Lagopas lagopus  8.343305 63.35766    19
 27: 2023/02/01   Male JUVENILE Lagopus lagopus  7.015809 62.97256    10
 28: 2023-02-01   MALE    ADULT Lagopas lagopus  7.249466 63.64190     5
 29:   02/02/23 FEMALE    Adult Lagopas lagopus  9.762441 61.59733     6
 30: 2023/02/01 Female Juvenile Lagopas lagopus  9.081167 62.09558     6
 31: 2023/02/01   MALE JUVENILE    Logopus muta  8.544149 64.01272    15
 32: 2023/02/01 FEMALE JUVENILE Lagopas lagopus  9.115873 64.69849     9
 33: 01-01-2023   male    ADULT    Lagopus matu  7.281479 63.76351    12
 34: 2023/02/01 female JUVENILE    Lagopus muta 10.688551 63.98931    15
 35:   02-01-23   Male Juvenile Lagopus lagopus  9.927145 62.94457     7
 36:   02-01-23   male Juvenile    Logopus muta  8.498186 62.40878     9
 37:   02-01-23 female Juvenile    Lagopus matu  8.993657 64.06921     0
 38: 2023-02-01 female    ADULT    Logopus muta  8.400518 63.67579     3
 39: 2023/02/01   Male    ADULT    Lagopus matu  8.671143 63.79903    18
 40: 01-01-2023 female        J    Lagopus matu  9.794615 61.83442     5
 41: 2023/02/01   MALE        A    Logopus muta  7.662123 63.20559    18
 42: 01-01-2023   male        A    Logopus muta  7.971045 64.32591    15
 43: 01-01-2023 female        J    Lagopus matu  8.777006 62.43949    11
 44:   02/02/23   Male Juvenile    Lagopus muta  8.228000 62.71882    16
 45: 01-01-2023 Female        J    Lagopus muta  8.912136 61.42190     5
 46: 01-01-2023   MALE Juvenile    Lagopus muta 10.286843 62.89537     7
 47: 2023/02/01   male    Adult    Logopus muta  9.195381 61.35946     6
 48:   02-01-23 Female        J    Lagopus matu  8.801430 62.92860     2
 49:   02/02/23 female        J Lagopas lagopus 11.148595 63.51963    10
 50:   02/02/23 female    ADULT Lagopas lagopus  7.861651 62.37019    12
 51: 2023-02-01 female        A    Lagopus muta  9.238828 62.88834     5
 52: 2023/02/01 female JUVENILE    Logopus muta  9.126381 63.92296    13
 53:   02-01-23 female Juvenile Lagopas lagopus 10.303237 62.86576     5
 54: 01-01-2023 female        A Lagopas lagopus  8.745229 62.17313    18
 55:   02-01-23 female        A    Logopus muta  8.691021 62.10421     6
 56:   02/02/23 female JUVENILE Lagopas lagopus  9.314176 62.15080    15
 57: 01-01-2023 Female Juvenile    Logopus muta  7.122930 62.32509    11
 58: 2023-02-01 Female        A Lagopas lagopus  9.117661 61.81606    18
 59: 01-01-2023   male        A Lagopas lagopus  9.800076 63.52459     3
 60: 2023/02/01 Female JUVENILE    Lagopus matu  9.263243 63.46659    12
 61:   02-01-23 Female    Adult Lagopas lagopus  9.432039 61.53335     7
 62: 2023-02-01   Male    Adult    Lagopus matu  7.910848 62.92433     1
 63:   02/02/23   Male        J    Logopus muta  9.092678 61.07257    13
 64: 2023/02/01   male        A Lagopus lagopus 10.627507 62.46044     9
 65: 2023/02/01   MALE        A    Lagopus matu  8.575023 62.45981    13
 66: 01-01-2023 female JUVENILE Lagopas lagopus 10.736562 64.37288     5
 67: 01-01-2023   MALE    ADULT Lagopas lagopus 10.644320 64.10796    14
 68:   02-01-23   MALE    ADULT Lagopus lagopus  8.442710 65.27996    12
 69:   02-01-23 FEMALE Juvenile Lagopas lagopus  7.970893 62.21394     6
 70:   02/02/23   male Juvenile    Lagopus muta  7.002591 62.35749     7
 71: 01-01-2023 FEMALE    ADULT Lagopus lagopus  9.516319 63.04347     6
 72: 01-01-2023 Female        A    Lagopus muta  8.313179 64.23023    12
 73: 2023-02-01 female        A Lagopas lagopus  7.678440 63.40045     6
 74:   02-01-23   male    ADULT    Lagopus matu  8.729332 60.78910     5
 75: 01-01-2023 Female    Adult    Logopus muta  9.753151 63.08899     8
 76:   02/02/23 FEMALE    Adult    Lagopus matu  7.873569 62.33233     8
 77: 01-01-2023   male Juvenile Lagopas lagopus  8.963270 62.15332     9
 78:   02/02/23   male    ADULT Lagopus lagopus  8.428166 64.55505     4
 79:   02/02/23 Female        A Lagopas lagopus  9.471109 61.53559    11
 80: 01-01-2023   MALE        J    Lagopus matu  9.236367 62.27483    12
 81: 2023-02-01 female    ADULT    Lagopus muta  8.939548 63.26092     3
 82:   02-01-23 female    ADULT    Logopus muta  9.227044 61.22400     5
 83: 2023-02-01 female JUVENILE    Lagopus muta  9.318695 62.20958    11
 84:   02/02/23 female Juvenile    Lagopus matu  8.708364 63.88290     7
 85:   02/02/23 female JUVENILE Lagopas lagopus  8.872903 63.71204     8
 86: 2023/02/01 female    Adult    Lagopus matu  7.703743 63.25247     1
 87: 2023-02-01 Female        A    Lagopus matu  9.127351 62.30380    11
 88: 2023-02-01 Female    Adult    Lagopus matu  9.523766 60.64250     8
 89: 2023/02/01 female        J Lagopas lagopus  9.181112 61.92349    12
 90:   02/02/23   MALE Juvenile Lagopas lagopus  7.702984 61.91841     4
 91:   02-01-23 female        J    Logopus muta  8.141424 63.80680     9
 92:   02-01-23   male Juvenile    Lagopus matu 11.014120 64.89251    18
 93: 01-01-2023   MALE JUVENILE    Lagopus muta  6.444234 64.92426     7
 94: 01-01-2023   male        J    Logopus muta  8.507807 63.49817     5
 95:   02-01-23 Female Juvenile    Lagopus matu  9.379068 62.59566     8
 96:   02-01-23   Male        J Lagopus lagopus  8.190334 61.91115    13
 97:   02-01-23   male        A    Lagopus matu  8.489750 63.48030     7
 98:   02/02/23 FEMALE    Adult    Lagopus muta 10.193635 62.98715    15
 99:   02/02/23   MALE        J    Logopus muta  8.798305 63.96787     5
100: 2023-02-01   MALE        A    Lagopus matu  7.846161 63.42758    14
           Date    SEX      age    Species Name       lat      lon count

Code style

What are attributes of good code?

Have a look at the “notReproducible.qmd” file

Tidyverse style guide

“Good coding style is like correct punctuation: you can manage without it, butitsuremakesthingseasiertoread.”

# Examples
day_one # Good
DayOne # Bad
# Avoid names of common functions
T <- FALSE # Bad
c <- 10 # Bad
mean <- function(x) sum(x) # Bad
# Space after a comma
x[, 1] # Good
x[,1] # Bad
# space after () in functions
function(x) {}# Good
function (x) {} # Bad
function(x){} # Bad

Useful package for style

library("styler")
style_text("a=3; 2", scope = "tokens")
a <- 3
2

What I think…

  1. It runs (on your computer)

  2. It runs (on my computer - without me having to do anything/much)

  3. It does what you expect it to do (even after 5 years)

  4. It is documented in some way

What Jenny Bryan thinks

If the first line of your R script is

setwd(“C:”)

I will come into your office and SET YOUR COMPUTER ON FIRE 🔥.

If the first line of your R script is

rm(list = ls())

I will come into your office and SET YOUR COMPUTER ON FIRE 🔥.

Sharing data

One of the biggest barriers to sharing data is a lack of standardisation and metadata

Standards

  • Standards provide the “rules” and “protocols” to share information
  • Standards enable interoperability of your data
  • Even if not sharing data openly (immediately) this is useful for working with collaborators
  • Sharing data depends on the consistent use of agreed standards.

Darwin Core

DWC-a

LivingNorwayR

Using open data

Culina, et al. Navigating the unfolding open data landscape in ecology and evolution. Nat Ecol Evol 2, 420–426 (2018). https://doi.org/10.1038/s41559-017-0458-2

Getting data through R (one way)

library(tidyverse)
library(RJSONIO)
library(EML)
## Using open ecology data
## Using packages other than the LivingNorwayR package
datasetKey <- "84b9a51f-ec2e-41dc-9d7a-1e3aa411b939"
dataset <- RJSONIO::fromJSON(paste0("http://api.gbif.org/v1/dataset/",
                                    datasetKey,"/endpoint"))
endpoint_url <- dataset[[1]]$url
datasetName=sub(".*r=", "", endpoint_url)
datsetName=sub("&v*.","", datasetName)
tempDirLoc <- tempdir()
localDataLoc <- file.path(tempDirLoc,datasetName)
download.file(endpoint_url, localDataLoc, mode = "wb")

## list the files in the archive
unzip(zipfile = localDataLoc, list = TRUE)
                   Name   Length                Date
1        occurrence.txt 25905555 2023-02-21 09:21:00
2               eml.xml     5080 2023-02-21 09:21:00
3 measurementorfact.txt  1487374 2023-02-21 09:21:00
4              meta.xml     3065 2023-02-21 09:21:00
occurence <- as_tibble(read.table(unz(localDataLoc, "occurrence.txt"),
                                  header=T,sep="\t", quote=""))
measure <- as_tibble(read.table(unz(localDataLoc, "measurementorfact.txt"),
                                header=T,sep="\t", quote=""))
## You need to unzip the eml before read_eml() will work
f <- unzip(localDataLoc, "eml.xml")
eml=EML::read_eml(f)

occurence
# A tibble: 34,112 x 32
        id modif~1 insti~2 colle~3 basis~4 dynam~5 occur~6 catal~7 occur~8   sex
     <int> <chr>   <chr>   <chr>   <chr>   <chr>     <int>   <int> <chr>   <int>
 1 5215659 2022-0~ NINA    Fiskme~ HumanO~ "\"{\"~ 5215659 5215659 ""         NA
 2 5294435 2022-0~ NINA    Fiskme~ HumanO~ "\"{\"~ 5294435 5294435 ""         NA
 3 5294765 2022-0~ NINA    Fiskme~ HumanO~ "\"{\"~ 5294765 5294765 ""         NA
 4 5814209 2020-1~ NINA    Fiskme~ HumanO~ "\"{\"~ 5814209 5814209 ""          2
 5 5814125 2020-0~ NINA    Fiskme~ Preser~ "\"{\"~ 5814125 5814125 "Ikke ~     1
 6 5814152 2020-0~ NINA    Fiskme~ Preser~ "\"{\"~ 5814152 5814152 "Fiske~     2
 7 5815714 2020-1~ NINA    Fiskme~ HumanO~ "\"{\"~ 5815714 5815714 "Fange~    NA
 8 5294610 2022-0~ NINA    Fiskme~ HumanO~ "\"{\"~ 5294610 5294610 ""         NA
 9 5814196 2020-0~ NINA    Fiskme~ Preser~ "\"{\"~ 5814196 5814196 "Ã…pne~     2
10 5823633 2022-0~ NINA    Fiskme~ HumanO~ "\"{\"~ 5823633 5823633 "Gjenf~     2
# ... with 34,102 more rows, 22 more variables: lifeStage <chr>,
#   associatedReferences <chr>, samplingProtocol <chr>, year <int>,
#   month <int>, day <int>, country <chr>, stateProvince <chr>, county <chr>,
#   locality <chr>, decimalLatitude <dbl>, decimalLongitude <dbl>,
#   coordinatePrecision <int>, scientificName <chr>, kingdom <chr>,
#   phylum <chr>, class <chr>, order <chr>, family <chr>, genus <chr>,
#   specificEpithet <chr>, vernacularName <chr>, and abbreviated variable ...

measure 
# A tibble: 68,224 x 4
        id measurementType measurementValue measurementUnit
     <int> <chr>           <chr>            <chr>          
 1 5215659 Weight          gram             "4500"         
 2 5294610 Weight          gram             "4500"         
 3 5294435 Weight          gram             "4800"         
 4 5294765 Weight          gram             "3500"         
 5 5814209 Weight          gram             "11200"        
 6 5814125 Weight          gram             "3600"         
 7 5814152 Weight          gram             "3900"         
 8 5815714 Weight          gram             ""             
 9 5814196 Weight          gram             "2500"         
10 5823633 Weight          gram             "10900"        
# ... with 68,214 more rows

eml$additionalMetadata$metadata$gbif$citation
[1] "Finstad, B. (2015): Fish tag database. v1. Norwegian Institute for Nature Research. Dataset/Occurrence. https://ipt.nina.no/ipt/resource?r=fiskmerk&amp;v=1.0"
eml$dataset$title
$lang
[1] "eng"

$title
[1] "National fish tag database"
eml$dataset$abstract
$para
[1] "National database of tagged salmonids (Atlantic salmon, brown trout and Arctic char). Carlin tags (smolt) and Lea tags (adult fish) from various tagging projects in Norway. Recapture of released fish."

# join measure to occurrence 
joined_dat<-occurence |> 
  left_join(measure)

joined_dat |> 
 data.table::data.table()
            id                modified institutionCode collectionCode
    1: 5215659 2022-02-02 13:07:58.973            NINA       Fiskmerk
    2: 5215659 2022-02-02 13:07:58.973            NINA       Fiskmerk
    3: 5294435 2022-02-02 13:07:58.973            NINA       Fiskmerk
    4: 5294435 2022-02-02 13:07:58.973            NINA       Fiskmerk
    5: 5294765 2022-02-02 13:07:58.973            NINA       Fiskmerk
   ---                                                               
68220: 5221563  2016-02-03 14:02:27.55            NINA       Fiskmerk
68221: 5221564  2016-02-03 14:02:27.55            NINA       Fiskmerk
68222: 5221564  2016-02-03 14:02:27.55            NINA       Fiskmerk
68223: 5290481  2016-02-03 14:02:27.55            NINA       Fiskmerk
68224: 5290481  2016-02-03 14:02:27.55            NINA       Fiskmerk
          basisOfRecord
    1: HumanObservation
    2: HumanObservation
    3: HumanObservation
    4: HumanObservation
    5: HumanObservation
   ---                 
68220: HumanObservation
68221: HumanObservation
68222: HumanObservation
68223: HumanObservation
68224: HumanObservation
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  dynamicProperties
    1: "{"tagSeries":"6758", "tagNumber":"6952", "tagLetter":"P   ", "tagSeriesStartNumber":"6801", "tagSeriesEndNumber":"6970", "tagSeriesFishStock":"", "TagSeriesFishCount":"170", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"Breivik på Sørøya", "tagSeriesTagFromDate":"Jul  1 1962 12:00AM", "tagSeriesTagToDate":"Jul 17 1962 12:00AM", "tagSeriesReleasedFromDate":"Jul  1 1962 12:00AM", "tagSeriesReleasedToDate":"Jul 17 1962 12:00AM", "tagSeriesReleasedPlace":"Breivik på Sørøya"}"
    2: "{"tagSeries":"6758", "tagNumber":"6952", "tagLetter":"P   ", "tagSeriesStartNumber":"6801", "tagSeriesEndNumber":"6970", "tagSeriesFishStock":"", "TagSeriesFishCount":"170", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"Breivik på Sørøya", "tagSeriesTagFromDate":"Jul  1 1962 12:00AM", "tagSeriesTagToDate":"Jul 17 1962 12:00AM", "tagSeriesReleasedFromDate":"Jul  1 1962 12:00AM", "tagSeriesReleasedToDate":"Jul 17 1962 12:00AM", "tagSeriesReleasedPlace":"Breivik på Sørøya"}"
    3:        "{"tagSeries":"6698", "tagNumber":"17591", "tagLetter":"NG- ", "tagSeriesStartNumber":"17564", "tagSeriesEndNumber":"17999", "tagSeriesFishStock":"Hunder", "TagSeriesFishCount":"435", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"Hunderfossen", "tagSeriesTagFromDate":"Jun 17 2005 12:00AM", "tagSeriesTagToDate":"Sep 26 2005 12:00AM", "tagSeriesReleasedFromDate":"Jun 17 2005 12:00AM", "tagSeriesReleasedToDate":"Sep 26 2005 12:00AM", "tagSeriesReleasedPlace":"Hunderfossen"}"
    4:        "{"tagSeries":"6698", "tagNumber":"17591", "tagLetter":"NG- ", "tagSeriesStartNumber":"17564", "tagSeriesEndNumber":"17999", "tagSeriesFishStock":"Hunder", "TagSeriesFishCount":"435", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"Hunderfossen", "tagSeriesTagFromDate":"Jun 17 2005 12:00AM", "tagSeriesTagToDate":"Sep 26 2005 12:00AM", "tagSeriesReleasedFromDate":"Jun 17 2005 12:00AM", "tagSeriesReleasedToDate":"Sep 26 2005 12:00AM", "tagSeriesReleasedPlace":"Hunderfossen"}"
    5:        "{"tagSeries":"6698", "tagNumber":"17588", "tagLetter":"NG- ", "tagSeriesStartNumber":"17564", "tagSeriesEndNumber":"17999", "tagSeriesFishStock":"Hunder", "TagSeriesFishCount":"435", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"Hunderfossen", "tagSeriesTagFromDate":"Jun 17 2005 12:00AM", "tagSeriesTagToDate":"Sep 26 2005 12:00AM", "tagSeriesReleasedFromDate":"Jun 17 2005 12:00AM", "tagSeriesReleasedToDate":"Sep 26 2005 12:00AM", "tagSeriesReleasedPlace":"Hunderfossen"}"
   ---                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
68220:                                                                      "{"tagSeries":"298", "tagNumber":"150865", "tagLetter":"B   ", "tagSeriesStartNumber":"150600", "tagSeriesEndNumber":"151000", "tagSeriesFishStock":"", "TagSeriesFishCount":"398", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"", "tagSeriesTagFromDate":"May 29 1971 12:00AM", "tagSeriesTagToDate":"", "tagSeriesReleasedFromDate":"May 29 1971 12:00AM", "tagSeriesReleasedToDate":"", "tagSeriesReleasedPlace":"EIRA"}"
68221:                                                                      "{"tagSeries":"298", "tagNumber":"150870", "tagLetter":"B   ", "tagSeriesStartNumber":"150600", "tagSeriesEndNumber":"151000", "tagSeriesFishStock":"", "TagSeriesFishCount":"398", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"", "tagSeriesTagFromDate":"May 29 1971 12:00AM", "tagSeriesTagToDate":"", "tagSeriesReleasedFromDate":"May 29 1971 12:00AM", "tagSeriesReleasedToDate":"", "tagSeriesReleasedPlace":"EIRA"}"
68222:                                                                      "{"tagSeries":"298", "tagNumber":"150870", "tagLetter":"B   ", "tagSeriesStartNumber":"150600", "tagSeriesEndNumber":"151000", "tagSeriesFishStock":"", "TagSeriesFishCount":"398", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"", "tagSeriesTagFromDate":"May 29 1971 12:00AM", "tagSeriesTagToDate":"", "tagSeriesReleasedFromDate":"May 29 1971 12:00AM", "tagSeriesReleasedToDate":"", "tagSeriesReleasedPlace":"EIRA"}"
68223:                                                 "{"tagSeries":"916", "tagNumber":"53395", "tagLetter":"NA  ", "tagSeriesStartNumber":"53000", "tagSeriesEndNumber":"53999", "tagSeriesFishStock":"EIRA", "TagSeriesFishCount":"998", "TagSeriesWildFarmed":"FarmedFish", "tagSeriesTagPlace":"", "tagSeriesTagFromDate":"May 29 1979 12:00AM", "tagSeriesTagToDate":"", "tagSeriesReleasedFromDate":"May 29 1979 12:00AM", "tagSeriesReleasedToDate":"", "tagSeriesReleasedPlace":"EIRA, MÃ\230RE OG ROMSDAL"}"
68224:                                                 "{"tagSeries":"916", "tagNumber":"53395", "tagLetter":"NA  ", "tagSeriesStartNumber":"53000", "tagSeriesEndNumber":"53999", "tagSeriesFishStock":"EIRA", "TagSeriesFishCount":"998", "TagSeriesWildFarmed":"FarmedFish", "tagSeriesTagPlace":"", "tagSeriesTagFromDate":"May 29 1979 12:00AM", "tagSeriesTagToDate":"", "tagSeriesReleasedFromDate":"May 29 1979 12:00AM", "tagSeriesReleasedToDate":"", "tagSeriesReleasedPlace":"EIRA, MÃ\230RE OG ROMSDAL"}"
       occurrenceID catalogNumber occurrenceRemarks sex lifeStage
    1:      5215659       5215659                    NA  Gytefisk
    2:      5215659       5215659                    NA  Gytefisk
    3:      5294435       5294435                    NA  Gytefisk
    4:      5294435       5294435                    NA  Gytefisk
    5:      5294765       5294765                    NA  Gytefisk
   ---                                                           
68220:      5221563       5221563                    NA     Smolt
68221:      5221564       5221564                    NA     Smolt
68222:      5221564       5221564                    NA     Smolt
68223:      5290481       5290481                    NA     Smolt
68224:      5290481       5290481                    NA     Smolt
       associatedReferences samplingProtocol year month day country
    1:            1962/9999                  1962     8   2  Norway
    2:            1962/9999                  1962     8   2  Norway
    3:             2007/042                  2006     6   1  Norway
    4:             2007/042                  2006     6   1  Norway
    5:             2007/038                  2006    11  15  Norway
   ---                                                             
68220:              71/   0    Spist av fugl 1971     7   1  Norway
68221:              71/   0    Spist av fugl 1971     7   1  Norway
68222:              71/   0    Spist av fugl 1971     7   1  Norway
68223:             2000/626    Spist av fugl 2000     6   1  Norway
68224:             2000/626    Spist av fugl 2000     6   1  Norway
          stateProvince     county             locality decimalLatitude
    1:         FINNMARK HAMMERFEST              Forsøl        70.72189
    2:         FINNMARK HAMMERFEST              Forsøl        70.72189
    3:          OPPLAND    GJÃ\230VIK    Mjøsa, Mjøsbrua        60.92901
    4:          OPPLAND    GJÃ\230VIK    Mjøsa, Mjøsbrua        60.92901
    5:          OPPLAND    GJÃ\230VIK         Mjøsa, Biri        60.95900
   ---                                                                 
68220: MÃ\230RE OG ROMSDAL     NESSET               NAUSTE        62.68768
68221: MÃ\230RE OG ROMSDAL     NESSET               NAUSTE        62.68768
68222: MÃ\230RE OG ROMSDAL     NESSET               NAUSTE        62.68768
68223: MÃ\230RE OG ROMSDAL     NESSET Eira utl.fugl 06.79?        62.68503
68224: MÃ\230RE OG ROMSDAL     NESSET Eira utl.fugl 06.79?        62.68503
       decimalLongitude coordinatePrecision scientificName  kingdom   phylum
    1:        23.806922                1000    Salmo salar Animalia Chordata
    2:        23.806922                1000    Salmo salar Animalia Chordata
    3:        10.658594                1000   Salmo trutta Animalia Chordata
    4:        10.658594                1000   Salmo trutta Animalia Chordata
    5:        10.592042                1000   Salmo trutta Animalia Chordata
   ---                                                                      
68220:         8.116772                1000    Salmo salar Animalia Chordata
68221:         8.116772                1000    Salmo salar Animalia Chordata
68222:         8.116772                1000    Salmo salar Animalia Chordata
68223:         8.131108                1000    Salmo salar Animalia Chordata
68224:         8.131108                1000    Salmo salar Animalia Chordata
                class         order     family genus specificEpithet
    1: Actinopterygii Salmoniformes Salmonidae Salmo           salar
    2: Actinopterygii Salmoniformes Salmonidae Salmo           salar
    3: Actinopterygii Salmoniformes Salmonidae Salmo          trutta
    4: Actinopterygii Salmoniformes Salmonidae Salmo          trutta
    5: Actinopterygii Salmoniformes Salmonidae Salmo          trutta
   ---                                                              
68220: Actinopterygii Salmoniformes Salmonidae Salmo           salar
68221: Actinopterygii Salmoniformes Salmonidae Salmo           salar
68222: Actinopterygii Salmoniformes Salmonidae Salmo           salar
68223: Actinopterygii Salmoniformes Salmonidae Salmo           salar
68224: Actinopterygii Salmoniformes Salmonidae Salmo           salar
       vernacularName measurementType measurementValue measurementUnit
    1:           Laks          Weight             gram            4500
    2:           Laks          Length              840              mm
    3:           Aure          Weight             gram            4800
    4:           Aure          Length              780              mm
    5:           Aure          Weight             gram            3500
   ---                                                                
68220:           Laks          Length                               mm
68221:           Laks          Weight             gram                
68222:           Laks          Length                               mm
68223:           Laks          Weight             gram                
68224:           Laks          Length                               mm

# Model weight by length
# need to fix the errors (wrong cols)
joined_dat_clean<-joined_dat |> 
  mutate(Value=case_when(
    measurementType=="Weight"~ measurementUnit,
    measurementType=="Length"~ measurementValue),
    unit=case_when(
      measurementType=="Weight"~ measurementValue,
      measurementType=="Length"~ measurementUnit
      
    )) |> 
  mutate(measurementValue=Value,
         measurementUnit=unit) |> 
  select(-c(Value, unit))

joined_dat_clean|> 
 data.table::data.table()
            id                modified institutionCode collectionCode
    1: 5215659 2022-02-02 13:07:58.973            NINA       Fiskmerk
    2: 5215659 2022-02-02 13:07:58.973            NINA       Fiskmerk
    3: 5294435 2022-02-02 13:07:58.973            NINA       Fiskmerk
    4: 5294435 2022-02-02 13:07:58.973            NINA       Fiskmerk
    5: 5294765 2022-02-02 13:07:58.973            NINA       Fiskmerk
   ---                                                               
68220: 5221563  2016-02-03 14:02:27.55            NINA       Fiskmerk
68221: 5221564  2016-02-03 14:02:27.55            NINA       Fiskmerk
68222: 5221564  2016-02-03 14:02:27.55            NINA       Fiskmerk
68223: 5290481  2016-02-03 14:02:27.55            NINA       Fiskmerk
68224: 5290481  2016-02-03 14:02:27.55            NINA       Fiskmerk
          basisOfRecord
    1: HumanObservation
    2: HumanObservation
    3: HumanObservation
    4: HumanObservation
    5: HumanObservation
   ---                 
68220: HumanObservation
68221: HumanObservation
68222: HumanObservation
68223: HumanObservation
68224: HumanObservation
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  dynamicProperties
    1: "{"tagSeries":"6758", "tagNumber":"6952", "tagLetter":"P   ", "tagSeriesStartNumber":"6801", "tagSeriesEndNumber":"6970", "tagSeriesFishStock":"", "TagSeriesFishCount":"170", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"Breivik på Sørøya", "tagSeriesTagFromDate":"Jul  1 1962 12:00AM", "tagSeriesTagToDate":"Jul 17 1962 12:00AM", "tagSeriesReleasedFromDate":"Jul  1 1962 12:00AM", "tagSeriesReleasedToDate":"Jul 17 1962 12:00AM", "tagSeriesReleasedPlace":"Breivik på Sørøya"}"
    2: "{"tagSeries":"6758", "tagNumber":"6952", "tagLetter":"P   ", "tagSeriesStartNumber":"6801", "tagSeriesEndNumber":"6970", "tagSeriesFishStock":"", "TagSeriesFishCount":"170", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"Breivik på Sørøya", "tagSeriesTagFromDate":"Jul  1 1962 12:00AM", "tagSeriesTagToDate":"Jul 17 1962 12:00AM", "tagSeriesReleasedFromDate":"Jul  1 1962 12:00AM", "tagSeriesReleasedToDate":"Jul 17 1962 12:00AM", "tagSeriesReleasedPlace":"Breivik på Sørøya"}"
    3:        "{"tagSeries":"6698", "tagNumber":"17591", "tagLetter":"NG- ", "tagSeriesStartNumber":"17564", "tagSeriesEndNumber":"17999", "tagSeriesFishStock":"Hunder", "TagSeriesFishCount":"435", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"Hunderfossen", "tagSeriesTagFromDate":"Jun 17 2005 12:00AM", "tagSeriesTagToDate":"Sep 26 2005 12:00AM", "tagSeriesReleasedFromDate":"Jun 17 2005 12:00AM", "tagSeriesReleasedToDate":"Sep 26 2005 12:00AM", "tagSeriesReleasedPlace":"Hunderfossen"}"
    4:        "{"tagSeries":"6698", "tagNumber":"17591", "tagLetter":"NG- ", "tagSeriesStartNumber":"17564", "tagSeriesEndNumber":"17999", "tagSeriesFishStock":"Hunder", "TagSeriesFishCount":"435", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"Hunderfossen", "tagSeriesTagFromDate":"Jun 17 2005 12:00AM", "tagSeriesTagToDate":"Sep 26 2005 12:00AM", "tagSeriesReleasedFromDate":"Jun 17 2005 12:00AM", "tagSeriesReleasedToDate":"Sep 26 2005 12:00AM", "tagSeriesReleasedPlace":"Hunderfossen"}"
    5:        "{"tagSeries":"6698", "tagNumber":"17588", "tagLetter":"NG- ", "tagSeriesStartNumber":"17564", "tagSeriesEndNumber":"17999", "tagSeriesFishStock":"Hunder", "TagSeriesFishCount":"435", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"Hunderfossen", "tagSeriesTagFromDate":"Jun 17 2005 12:00AM", "tagSeriesTagToDate":"Sep 26 2005 12:00AM", "tagSeriesReleasedFromDate":"Jun 17 2005 12:00AM", "tagSeriesReleasedToDate":"Sep 26 2005 12:00AM", "tagSeriesReleasedPlace":"Hunderfossen"}"
   ---                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
68220:                                                                      "{"tagSeries":"298", "tagNumber":"150865", "tagLetter":"B   ", "tagSeriesStartNumber":"150600", "tagSeriesEndNumber":"151000", "tagSeriesFishStock":"", "TagSeriesFishCount":"398", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"", "tagSeriesTagFromDate":"May 29 1971 12:00AM", "tagSeriesTagToDate":"", "tagSeriesReleasedFromDate":"May 29 1971 12:00AM", "tagSeriesReleasedToDate":"", "tagSeriesReleasedPlace":"EIRA"}"
68221:                                                                      "{"tagSeries":"298", "tagNumber":"150870", "tagLetter":"B   ", "tagSeriesStartNumber":"150600", "tagSeriesEndNumber":"151000", "tagSeriesFishStock":"", "TagSeriesFishCount":"398", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"", "tagSeriesTagFromDate":"May 29 1971 12:00AM", "tagSeriesTagToDate":"", "tagSeriesReleasedFromDate":"May 29 1971 12:00AM", "tagSeriesReleasedToDate":"", "tagSeriesReleasedPlace":"EIRA"}"
68222:                                                                      "{"tagSeries":"298", "tagNumber":"150870", "tagLetter":"B   ", "tagSeriesStartNumber":"150600", "tagSeriesEndNumber":"151000", "tagSeriesFishStock":"", "TagSeriesFishCount":"398", "TagSeriesWildFarmed":"WildFish", "tagSeriesTagPlace":"", "tagSeriesTagFromDate":"May 29 1971 12:00AM", "tagSeriesTagToDate":"", "tagSeriesReleasedFromDate":"May 29 1971 12:00AM", "tagSeriesReleasedToDate":"", "tagSeriesReleasedPlace":"EIRA"}"
68223:                                                 "{"tagSeries":"916", "tagNumber":"53395", "tagLetter":"NA  ", "tagSeriesStartNumber":"53000", "tagSeriesEndNumber":"53999", "tagSeriesFishStock":"EIRA", "TagSeriesFishCount":"998", "TagSeriesWildFarmed":"FarmedFish", "tagSeriesTagPlace":"", "tagSeriesTagFromDate":"May 29 1979 12:00AM", "tagSeriesTagToDate":"", "tagSeriesReleasedFromDate":"May 29 1979 12:00AM", "tagSeriesReleasedToDate":"", "tagSeriesReleasedPlace":"EIRA, MÃ\230RE OG ROMSDAL"}"
68224:                                                 "{"tagSeries":"916", "tagNumber":"53395", "tagLetter":"NA  ", "tagSeriesStartNumber":"53000", "tagSeriesEndNumber":"53999", "tagSeriesFishStock":"EIRA", "TagSeriesFishCount":"998", "TagSeriesWildFarmed":"FarmedFish", "tagSeriesTagPlace":"", "tagSeriesTagFromDate":"May 29 1979 12:00AM", "tagSeriesTagToDate":"", "tagSeriesReleasedFromDate":"May 29 1979 12:00AM", "tagSeriesReleasedToDate":"", "tagSeriesReleasedPlace":"EIRA, MÃ\230RE OG ROMSDAL"}"
       occurrenceID catalogNumber occurrenceRemarks sex lifeStage
    1:      5215659       5215659                    NA  Gytefisk
    2:      5215659       5215659                    NA  Gytefisk
    3:      5294435       5294435                    NA  Gytefisk
    4:      5294435       5294435                    NA  Gytefisk
    5:      5294765       5294765                    NA  Gytefisk
   ---                                                           
68220:      5221563       5221563                    NA     Smolt
68221:      5221564       5221564                    NA     Smolt
68222:      5221564       5221564                    NA     Smolt
68223:      5290481       5290481                    NA     Smolt
68224:      5290481       5290481                    NA     Smolt
       associatedReferences samplingProtocol year month day country
    1:            1962/9999                  1962     8   2  Norway
    2:            1962/9999                  1962     8   2  Norway
    3:             2007/042                  2006     6   1  Norway
    4:             2007/042                  2006     6   1  Norway
    5:             2007/038                  2006    11  15  Norway
   ---                                                             
68220:              71/   0    Spist av fugl 1971     7   1  Norway
68221:              71/   0    Spist av fugl 1971     7   1  Norway
68222:              71/   0    Spist av fugl 1971     7   1  Norway
68223:             2000/626    Spist av fugl 2000     6   1  Norway
68224:             2000/626    Spist av fugl 2000     6   1  Norway
          stateProvince     county             locality decimalLatitude
    1:         FINNMARK HAMMERFEST              Forsøl        70.72189
    2:         FINNMARK HAMMERFEST              Forsøl        70.72189
    3:          OPPLAND    GJÃ\230VIK    Mjøsa, Mjøsbrua        60.92901
    4:          OPPLAND    GJÃ\230VIK    Mjøsa, Mjøsbrua        60.92901
    5:          OPPLAND    GJÃ\230VIK         Mjøsa, Biri        60.95900
   ---                                                                 
68220: MÃ\230RE OG ROMSDAL     NESSET               NAUSTE        62.68768
68221: MÃ\230RE OG ROMSDAL     NESSET               NAUSTE        62.68768
68222: MÃ\230RE OG ROMSDAL     NESSET               NAUSTE        62.68768
68223: MÃ\230RE OG ROMSDAL     NESSET Eira utl.fugl 06.79?        62.68503
68224: MÃ\230RE OG ROMSDAL     NESSET Eira utl.fugl 06.79?        62.68503
       decimalLongitude coordinatePrecision scientificName  kingdom   phylum
    1:        23.806922                1000    Salmo salar Animalia Chordata
    2:        23.806922                1000    Salmo salar Animalia Chordata
    3:        10.658594                1000   Salmo trutta Animalia Chordata
    4:        10.658594                1000   Salmo trutta Animalia Chordata
    5:        10.592042                1000   Salmo trutta Animalia Chordata
   ---                                                                      
68220:         8.116772                1000    Salmo salar Animalia Chordata
68221:         8.116772                1000    Salmo salar Animalia Chordata
68222:         8.116772                1000    Salmo salar Animalia Chordata
68223:         8.131108                1000    Salmo salar Animalia Chordata
68224:         8.131108                1000    Salmo salar Animalia Chordata
                class         order     family genus specificEpithet
    1: Actinopterygii Salmoniformes Salmonidae Salmo           salar
    2: Actinopterygii Salmoniformes Salmonidae Salmo           salar
    3: Actinopterygii Salmoniformes Salmonidae Salmo          trutta
    4: Actinopterygii Salmoniformes Salmonidae Salmo          trutta
    5: Actinopterygii Salmoniformes Salmonidae Salmo          trutta
   ---                                                              
68220: Actinopterygii Salmoniformes Salmonidae Salmo           salar
68221: Actinopterygii Salmoniformes Salmonidae Salmo           salar
68222: Actinopterygii Salmoniformes Salmonidae Salmo           salar
68223: Actinopterygii Salmoniformes Salmonidae Salmo           salar
68224: Actinopterygii Salmoniformes Salmonidae Salmo           salar
       vernacularName measurementType measurementValue measurementUnit
    1:           Laks          Weight             4500            gram
    2:           Laks          Length              840              mm
    3:           Aure          Weight             4800            gram
    4:           Aure          Length              780              mm
    5:           Aure          Weight             3500            gram
   ---                                                                
68220:           Laks          Length                               mm
68221:           Laks          Weight                             gram
68222:           Laks          Length                               mm
68223:           Laks          Weight                             gram
68224:           Laks          Length                               mm

weight_length<-joined_dat_clean |> 
  filter(vernacularName=="Laks") |> 
  select(id,
         measurementType, measurementValue) |> 
  pivot_wider(id, names_from =measurementType, values_from = measurementValue )

weight_length |> 
  mutate(Weight=as.numeric(Weight)) |> 
  mutate(Length=as.numeric(Length)) |> 
  ggplot(aes(Weight, Length)) +
  geom_point(colour="darksalmon")+
  theme_classic()